The novel satellite navigation system is the self-manufactured system by China. Its leading feature is to suppress interference in the MIMO system. In this paper, an anti-interference algorithm of the half-blind MIMO channel in the novel satellite navigation system, employing MATLAB, is proposed. The anti-interference performance of the half-blind channel is compared to that of the all-known channel under the conditions of changing the location of the interference, changing the number of the receive antennas and changing the array pattern. The simulation results reflect the practicability and superiority of the half-blind channel anti-interference algorithm.